Side Effects of Flagyl (Metronidazole)

This antibiotic is used to treat infections and pouchitis in j-pouches

Flagyl is a type of antibiotic and an antiprotozoal medication that is used to treat bacterial infections in the body. The generic name for this antibiotic is metronidazole, and it also may be sold under names such as Metrogel, Metrolotion, Noritate, Nuvessa, and Vandazole. Flagyl may be used to treat infections occurring in the skin, reproductive organs, and the digestive tract. It is often taken as a capsule, but it can also be applied topically or vaginally, or administered as an IV in a hospital or healthcare provider’s office.

Common Side Effects of Flagyl (Metronidazole)
Verywell / Gary Ferster


Flagyl is sometimes used to treat Crohn’s disease, which is one form of inflammatory bowel disease (IBD), especially when the disease is affecting the perianal area or only the colon (large intestine). It may also be used to treat pouchitis, which is a poorly-understood condition that occurs in people who have had surgery to remove their large intestine and create an internal pouch from the small intestine, which is called a j-pouch. Pouchitis tends to occur more often in people who had the surgery to treat ulcerative colitis than in people who had the surgery to treat another condition in the colon, such as familial adenomatous polyposis (FAP).

Flagyl is also used to treat an infection in the digestive tract with a bacteria called Clostridioides difficile (formerly called Clostridium difficile, commonly called C. diff). C. diff infections are becoming increasingly prevalent and are especially dangerous when they occur in people who have IBD. For treating pouchitis and C. diff, Flagyl is sometimes taken for long periods of time, and perhaps along with another antibiotic, or alternating with another antibiotic.

Flagyl is also used in combination with other drugs to treat an infection with Helicobacter pylori. H. pylori infects the stomach and can lead to stomach ulcers.

Flagyl And Alcohol

It is extremely important that people who take Flagyl not drink alcoholic beverages until at least 3 days after stopping the drug. Flagyl affects the way alcohol is broken down, and that leads to symptoms of nausea and vomiting, which can be severe.

Common Side Effects

Check with your healthcare provider if any of the following side effects continue or are bothersome:

  • diarrhea
  • dizziness or light-headedness
  • headache
  • loss of appetite
  • nausea or vomiting
  • stomach pain or cramps
  • unpleasant or sharp metallic taste

Check With Your Healthcare Provider

Check with your healthcare provider if you have any of the following side effects, which may be caused by hypersensitivity to the medication:

  • any vaginal irritation, discharge, or dryness not present before use of this medicine
  • dryness of the mouth
  • clumsiness or unsteadiness
  • mood or other mental changes
  • skin rash, hives, redness, or itching
  • sore throat and fever
  • stomach and back pain (severe)

For injection form:

  • Pain, tenderness, redness, or swelling over the vein in which the medicine is given

Notify Your Healthcare Provider Immediately

It’s not common, but some people experience a tingling in their hands and feet when taking Flagyl. If that happens, stop taking the drug immediately and call the healthcare provider to figure out what to do next.

Less common: Numbness, tingling, pain, or weakness in hands or feet

Rare: Convulsions (seizures)

Other Important Considerations

All antibiotics can reduce the effectiveness of oral contraceptives (“the pill”), so women using this as their birth control method should use a backup method until after finishing the course of antibiotics.

Flagyl can also sometimes cause urine to turn dark brown, but this is not dangerous and it goes away after the drug is stopped.

Flagyl, and all other antibiotics, should always be taken until the prescribed dose is finished. If there are concerns about the potential adverse effects of this or any other drug, check with a pharmacist and/or healthcare provider before discontinuing it.

Other side effects not listed above may also occur in some patients. Check with a healthcare provider about any other effects that occur. This information is meant only as a guideline—always consult a healthcare provider or pharmacist for complete information about prescription medications.

3 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. Schieffer KM, Williams ED, Yochum GS, Koltun WA. Review article: the pathogenesis of pouchitis. Aliment Pharmacol Ther. 2016;44(8):817-835. doi:10.1111/apt.13780

  2. Chey WD, Leontiadis GI, Howden CW, Moss SF. ACG clinical guideline: treatment of Helicobacter pylori infection. Am J Gastroenterol. 2017;112(2):212-239. doi:10.1038/ajg.2016.563

  3. National Library of Medicine. DailyMed. FLAGYL- metronidazole tablet, film coated [drug label].

By Amber J. Tresca
Amber J. Tresca is a freelance writer and speaker who covers digestive conditions, including IBD. She was diagnosed with ulcerative colitis at age 16.